|
| Status |
Public on Sep 07, 2017 |
| Title |
Liver_control_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Artibeus jamaicensis |
| Characteristics |
tissue: Liver
treatment: 100 ul of sterile DPBS to act as negative controls
|
| Treatment protocol |
Two Jamaican fruit bats were inoculated with 100 μl of sterile DPBS to act as negative controls, and two bats were inoculated with 100 μl containing 106 TCID50 Tacaribe virus. Negative control bats were euthanized at the end of the experimental period (45 days p.i,), while TCRV inoculated bats were euthanized as they became moribund. Kidney, liver, and spleen samples were collected in RNAlater and used for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organ samples were homogenized using zirconia/silica beads and a mini-bead-beater and RNA was extracted using QiaShredder columns and RNeasy minikits.
RNA libraries were prepared for sequencing using the Kapa Biosystems stranded-RNA sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FastX toolkit to filter adaptors, non-coding RNA, low quality reads, and raw reads with average lengths less than 20 bases
The Trinity program was employed for De novo transcriptome assembly. Parameters used were as follows: minimum contig length= 300 and minimum kmer coverage=2. The remaining contigs were further processed with Bowtie and RSEM
Genome_build: denovo
Supplementary_files_format_and_content: The De novo transcriptome assembly for bat (Trinity.fasta) was generated from pooled RNA-seq data from the different organ tissue
|
| |
|
| Submission date |
Dec 07, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Diana Lea Gerrard |
| E-mail(s) |
dgerrard@uvm.edu
|
| Organization name |
University of Vermont
|
| Department |
Cellular molecular and biomedical sciences
|
| Lab |
Seth Frietze, PhD
|
| Street address |
89 Beaumont Ave C141C Given
|
| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
| |
|
| Platform ID |
GPL21218 |
| Series (1) |
| GSE75771 |
Transcriptome Profiling of a Pathogenic Response to a Viral Infection in Jamaican Fruit Bats Artibeus jamaicensis Experimentally Infected With Tacaribe Virus |
|
| Relations |
| SRA |
SRX1471424 |
| BioSample |
SAMN04326868 |
